Anything from a half-an inch to an inch down will start showing reduced oxygen in any but too-large gravels, but whether or not it has any excess build-up of organics will depend on how many roots are in the area. Large unplanted areas need deep vacuuming just as they do in unplanted tanks, and for the same reasons.
Captain Hook's problem is all but certainly due to the wood blocking water flow in the area (inevitable, but correctable. He knows now to vacuum the areas periodically). Planting strongly rooted plants right behind the wood could help as well (sword, Crinum, larger Crypts, etc.).